NAME¶

SYNOPSIS

micro_razers [OPTIONS] <GENOME FILE> <READS FILE>

DESCRIPTION

MicroRazerS uses a prefix-based mapping strategy to map small RNA reads possibly containing 3' adapter sequence.

Input to MicroRazerS is a reference genome file and a file with single-end reads. Use - to read the reads from stdin.

(c) Copyright 2009 by Anne-Katrin Emde.

REQUIRED ARGUMENTS

ARGUMENT 0 INPUT_FILE

A reference genome file. Valid filetypes are: .sam, .raw, .gbk, .frn, .fq, .fna, .ffn, .fastq, .fasta, .faa, .fa, .embl, and .bam.

READS List of INPUT_FILE's

Either one (single-end) or two (paired-end) read files. Valid filetypes are: .sam, .raw, .gbk, .frn, .fq, .fna, .ffn, .fastq, .fasta, .faa, .fa, .embl, and .bam.

OPTIONS

-h, --help

Display the help message.

--version-check BOOL

Turn this option off to disable version update notifications of the application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: 1.

--version

Display version information.

Main Options::

-o, --output OUTPUT_FILE

Change output filename. (use - to dump to stdout in razers format) Default: <READS FILE>.razers. Valid filetypes are: .sam and .razers.

-rr, --recognition-rate DOUBLE

set the percent recognition rate In range [80..100]. Default: 100.

-sL, --seed-length INTEGER

seed length In range [10..inf]. Default: 16.

-sE, --seed-error

allow for one error in the seed

-f, --forward

map reads only to forward strands.

-r, --reverse

map reads only to reverse strands.

-mN, --match-N

'N' matches with all other characters

-m, --max-hits INTEGER

output only NUM of the best hits In range [1..inf]. Default: 100.

-pa, --purge-ambiguous

purge reads with more than max-hits best matches

-lm, --low-memory

decrease memory usage at the expense of runtime

-v, --verbose

verbose mode

-vv, --vverbose

very verbose mode

Output Options::

-a, --alignment

dump the alignment for each match

-gn, --genome-naming INTEGER

Select how genomes are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0.

-rn, --read-naming INTEGER

Select how reads are named. 0 = use Fasta id, 1 = enumerate beginning with 1. In range [0..1]. Default: 0.

-so, --sort-order INTEGER

Select how matches are sorted. 0 = read number, 1 = genome position. In range [0..1]. Default: 0.

-pf, --position-format INTEGER

Select begin/end position numbering (see Coordinate section below). 0 = gap space, 1 = position space. In range [0..1]. Default: 0.

VERSION

Last update: micro_razers version: 1.0.9 [tarball] SeqAn version: 2.3.1